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The PLATON/TwinRotMat Tool for Twinning Detection
Ton SpekNational Single Crystal
Service Facility,
Utrecht University,
The Netherlands.
Delft, 29-Sept-2008
Viewpoints on Twinning (I)
• Macroscopic - Mineralogy- Intergrowth
• Microscopic - Extinction pattern under polarized light
• Ways of Formation - Deformation, Growth, Pressure, T
• Molecular level - Local Pseudo Symmetry
Viewpoints on Twinning (II)
• Data collection
• Processing Procedures
• Refinement Procedures
• Detection of Twinning
• Twinning Matrix
• See: http://www.cryst.chem.uu.nl/lutz/twin/twin_lit.html
Twinning Symptoms
• Not all reflections fit in a single lattice• Statistics <|E2-1|> small etc.• Problems to solve the structure• Poor refinement• wR2 >> 2 * R1• Ghost peaks at chemically impossible positions.• High value of the second Wght parameter• Fobs >> Fcalc for a large number of reflections• Etc.
Twinning Matrix (I)
Non-Merohedral Twins
• Partially overlapped reciprocal lattices
• Problem now largely solved with current area detector images (CCD)
• Twinning Matrix from indexing software (Dirax, CellNow etc.)
• Adequate integration software
(HKLF 5)
Twinning Matrix (II)
(Pseudo)-Merohedral Twins:
• Overlapping Lattices(Lattice symmetry >> Symmetry of the Structure)
• Symmetry elements of the lattice but not of the structure are possible twinning laws.
• Coset Decomposition
Possible Twin laws to be tested
H.D.Flack (1987). J. Appl. Cryst. A43, 564-568.
Twinning Matrix (III)
Diagnostic analysis of Fo/Fc CIF
• ROTAX (Simon Parsons & B. Gould)Lists possible twin laws from analysis of poorly
fitting reflections with Fobs >> Fcalc in .fcfCooper et al., (2002). J.Appl.Cryst., 35, 168-174
• PLATON/TwinRotMat • Automatically lists the applicable twin law(s) +
predicted BASF & R-drop(s)(from .cif & .fcf data)
TwinRotMat Example (I)
• Study of the structure of cyclohexanone oxime. (ZZZVPO)
• Originally published as disordered in P3 with R = 9.25 %.(Acta Cryst. (2001),B57,705)• But no signs of disorder in the diffraction data.• Alternative not disordered solution in Space
Group P-3.• Refinement with three independent oxime
molecules converged to an unsatisfactorily R= 20%. ORTEP
P-3
R = 20% Model
TwinRotMat Example (II)
• Noisy difference map etc.
• H’s on O not found
• Twinning ?
• Run PLATON/TwinRotMat on the CIF/FCF of the converged R = 20% model.
TwinRotMat Example (III)
• Result: (shown in next slide).• Twin law with an estimate of the twinning
fraction and the estimated drop in R-value when applied
• Note:- Green entries indicate significant R-drop
TwinRotMat Example (IV)
• An HKLF5 file can be generated by clicking on ‘HKLF5-gener’ after selecting the matrices to be used.
or
• TWIN/BASF refinement with the proposed matrix.
• Display the overlap of the two lattices related by the twin law (2-fold axis parallel to c) as viewed down the c-axes.
P-3
55:45 twin
R=3.44
Ideas behind the Algorithm
• Reflections effected by twinning show-up in the least-squares refinement with F(obs) >> F(calc)
• Overlapping reflections necessarily have the same Theta value within a certain tolerance.
• Generate a list of implied possible twin axes based on the above observations.
• Test each proposed twin law for its effect on R.
Possible Twin Axis
H H’
H” = H + H’
Strong reflection H’ with theta close to theta of reflection H
Candidate twinning axis(Normalize !)
Reflection withF(obs) >> F(calc)
What about trillings ?
Example: [PrFe(CN)6(H2O)2].2H2OLanger et al. (2004).Acta Cryst., C60,1104.
Space group Cmcm (R-int = 0.15)Pseudo hexagonal (R-int = 0.16) Refinement (via model in P21 etc.) in Cmcmwith TWIN -.5 .5 0 –1.5 -.5 0 0 0 1 3 R = 0.017, wR2 = 0.039Fractions: 0.6, 0.2, 0.2
TwinRotMat Analysis
• Starting model is the published structure in Cmcm without twinning.
• R = 0.15, wR2 = 0.37
• Large residual density peaks.
• TwinRotMat
HKLF 5 Generation
• Use the two rotations about the proposed direct lattice directions [1 1 0] & [1 –1 0]
They have a slightly better overlap than the corresponding reciprocal lattice directions [1 3 0]* & [1 –3 0]*
• See overlap in reciprocal space
Refinement Results
• Based on HKLF5 file with two matrices
• R = 0.02
• Twin parts 0.6, 0.2, 0.2
• Thus equivalent with the thrilling description.
FCF-VALIDATION
Forthcoming:
Automatic twinning detection as part of the
IUCr CheckCif procedure
- Detection of ignored twinning
- Detection of Applied Twinning Correction without being reported
(Already available via PLATON/Check)
Example of Unreported Twinning (I)
• Sadiq-ur-Rehman et al. (2008). Acta Cryst. E64, e26 & (2007). E63, m2329.
• Sn3(CH3)9Cl(NO3) reinterpreted as
Sn3(CH3)9Cl(CO3)• But: Still no mention of twinning ! In the
paper nor in the CIF (although a correction for twinning was applied)
• No CIF datanames defined yet for twinning• CIF/FCF Validation ALERT
Example of Unreported Twinning (II)
Residual Problems
Getting a Preliminary Model from
• a (pseudo-)merohedrally twinned dataset
• Integrated data corresponding to a larger twin lattice rather than the smaller lattice of the structure (e.g. oC <-> mP)
(Sometimes, but not always showing non space group extinctions)
Concluding Remarks
TwinRotMat• Points to the effective twin laws to be included in
the structure refinement given a partially refined structure model
• Offers a diagnostic tool for possibly missed twinning as part crystal structure validation
• Nowadays possibly less important for the detection of non-merohedral twinning (CCD)
(But cases of missed non-merohedral twinningstill arrive for publication)
Additional Info
http://www.cryst.chem.uu.nl (including a copy of this powerpoint presentation)
Thanks
for your attention !!